create_beauti_options_v2_6 {beautier}

Function to create the BEAUti options for version 2.6.

Description

Function to create the BEAUti options for version 2.6, by calling create_beauti_options.

Usage

create_beauti_options_v2_6(
  beast2_version = "2.6",
  sequence_indent = 8,
  nucleotides_uppercase = FALSE,
  status = "",
  namespace = get_default_beast_namespace_v2_6(),
  required = ""
)

Arguments

beast2_version

the BEAST2 version

sequence_indent

the number of spaces the XML sequence lines are indented

nucleotides_uppercase

must the nucleotides of the DNA sequence be in uppercase?

status

the BEAUti status

namespace

the 'namespace' XML element in the 'beast' XML tag.

required

things that may be required, for example BEAST v2.5.0

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

See Also

see create_beauti_options_v2_4 for using the older v2.4

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_6()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}